Journal home
Advance online publication
Current issue
Archive
Press releases
Supplements
Focuses
Conferences
Guide to authors
Online submissionOnline submission
Permissions
For referees
Free online issue
Contact the journal
Subscribe
Advertising
work@npg
naturereprints
About this site
For librarians
 
NPG Resources
Bioentrepreneur
Nature Reviews Drug Discovery
Nature
Nature Medicine
Nature Genetics
Nature Reviews Genetics
Nature Methods
Nature Chemical Biology
news@nature.com
Clinical Pharmacology & Therapeutics
Nature Conferences
NPG Subject areas
Biotechnology
Cancer
Chemistry
Clinical Medicine
Dentistry
Development
Drug Discovery
Earth Sciences
Evolution & Ecology
Genetics
Immunology
Materials Science
Medical Research
Microbiology
Molecular Cell Biology
Neuroscience
Pharmacology
Physics
Browse all publications
Analysis
Nature Biotechnology  23, 137 - 144 (2005)
Published online: 6 January 2005; | doi:10.1038/nbt1053

Assessing computational tools for the discovery of transcription factor binding sites

Martin Tompa1, 2, Nan Li1, Timothy L Bailey3, George M Church4, Bart De Moor5, Eleazar Eskin6, Alexander V Favorov7, 8, Martin C Frith9, Yutao Fu9, W James Kent10, Vsevolod J Makeev7, 8, Andrei A Mironov7, 11, William Stafford Noble1, 2, Giulio Pavesi12, Graziano Pesole13, Mireille Régnier14, Nicolas Simonis15, Saurabh Sinha16, Gert Thijs5, Jacques van Helden15, Mathias Vandenbogaert14, Zhiping Weng9, Christopher Workman17, Chun Ye18 & Zhou Zhu4

1  Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195-2350, USA.

2  Department of Genome Sciences, Box 357730, University of Washington, Seattle, Washington 98195-7730, USA.

3  Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia.

4  Department of Genetics and Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

5  ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium.

6  Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.

7  State Scientific Centre 'GosNIIGenetica,' 1st Dorozhny pr. 1, Moscow, 117545, Russia.

8  Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia.

9  Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.

10  Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.

11  Department of Bioengineering and Bioinformatics, Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-33, Moscow 119992, Russia.

12  Department of Computer Science and Communication (D.I.Co), University of Milan, Milan, Italy.

13  Department of Biomolecular Science and Biotechnology, University of Milan, Milan, Italy.

14  INRIA Rocquencourt, Domaine de Voluceau B.P. 105, 78153 Le Chesnay, France.

15  SCMB-Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium.

16  Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.

17  Department of Bioengineering, University of California, San Diego, California 92093, USA.

18  Bioinformatics Program, University of California, San Diego, California 92093, USA.

Correspondence should be addressed to Martin Tompa tompa@cs.washington.edu
The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

 Top
Abstract
Previous | Next
Table of contents
Full textFull text
Download PDFDownload PDF
Send to a friendSend to a friend
Save this linkSave this link

Open Innovation Challenges

naturejobs

Figures & Tables
Supplementary info
Export citation
natureproducts

Search buyers guide:

 
ADVERTISEMENT
 
Nature Biotechnology
ISSN: 1087-0156
EISSN: 1546-1696
Journal home | Advance online publication | Current issue | Archive | Press releases | Supplements | Focuses | Conferences | For authors | Online submission | Permissions | For referees | Free online issue | About the journal | Contact the journal | Subscribe | Advertising | work@npg | naturereprints | About this site | For librarians
Nature Publishing Group, publisher of Nature, and other science journals and reference works©2005 Nature Publishing Group | Privacy policy